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This thread is old, but it looks like the most appropriate place to ask. Has there been update in that field? I'm using combinations of hac2l/hactool/hactoolnet and hacpack to merge base and update. But this seems broken since around firmware 20.0, where unknown sections (probably a desync in parsing) are found in NCAs.
However, I see some people, like FitGirl, able to perform these merges, so there must be updated tools?
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